QSESTIMATE procedure

Calculates QTL effects in single-environment trials (M.P. Boer, M. Malosetti, S.J. Welham & J.T.N.M. Thissen).

Options

Parameters

Description

QSESTIMATE fits a final QTL model to estimate QTL effects in single-environment trials. It uses single observations per genotype as phenotypic data. The response variable must be specified by the TRAIT parameter, and the genotypes by the GENOTYPES parameter.The POPULATIONTYPE option must be set to specify the population from which the genotypes are derived. For recombinant inbred lines (POPULATIONTYPE = RIL), the NGENERATIONS option, must be set to supply the number of generations. For backcross inbred lines (POPULATIONTYPE = BCxSy), the NBACKCROSSES and NSELFINGS options must be set to define the number of backcrosses to the first parent and the number of selfings, respectively.

Molecular information must be provided in the form of additive genetic predictors stored in variates and supplied, in a pointer, by the ADDITIVEPREDICTORS parameter. Non-additive effects can be included in the model by specifying dominance genetic predictors using the DOMINANCEPREDICTORS parameter (e.g. in a F2 population). In the case of segregating F1 populations (outbreeders) two sets of additive genetic predictors must be specified, the maternal ones by the ADDITIVEPREDICTORS parameter, and the paternal ones by the ADD2PREDICTORS parameter. The corresponding map information for the genetic predictors must be given by the CHROMOSOMES and POSITIONS parameters. The labels for the loci can be supplied by the IDLOCI parameter, and the labels for the genotypes in the marker data can be supplied by the IDMGENOTYPES parameter. If IDMGENOTYPES is set, the match between the genotypes in the phenotypic and in the marker data will be checked. The IDPARENTS parameter can supply labels to identify the parents.

The QTL model assumes genotypes as random and QTLs as fixed effects. Extra fixed effects can be specified using the FIXED option. The QTLSELECTED parameter must specify the set of QTLs, in the form of a variate containing the index number of the positions where the QTLs are located. When the DOMINANCEPREDICTORS parameter is set, the DOMSELECTED parameter supplies a logical variate containing one if the dominance predictor of the corresponding marker must be present in the model, and zero if the dominance predictor of the corresponding marker must be absent in the model. If DOMINANCEPREDICTORS is set but DOMSELECTED is not set, all the dominance predictors are included.

The MVINCLUDE, MAXCYCLE and WORKSPACE options operate in the same way as these options of the REML directive. The UNITERROR parameter allows uncertainty on the trait means (derived from individual unit or plot error) to be specified to include in the random model; by default this is omitted. The UNITFACTOR option allows the factor that is needed to define the unit-error term to be saved (this would be needed, for example, to save information later about the term using VKEEP).

The PRINT option specifies the output to be displayed. The summary setting prints the information about the QTLs retained in the model, and the other settings correspond to those in the PRINT option of the REML directive. To be able to calculate the explained variance in the summary, the option POPULATIONTYPE must be set.

The QTL effects and their standard errors can be saved by the QEFFECTS and QSE parameters, respectively, and the fitted values and residuals can be saved by the FITTEDVALUES and RESIDUALS parameters. These are saved in pointers that contain a single variate if only the ADDITIVEPREDICTORS parameter is specified, or two or three variates if the DOMINANCEPREDICTORS and/or ADD2PREDICTORS parameters are also specified. The Wald statistics, degrees of freedom and probabilities can be saved by the parameters WALDSTATISTICS, DFWALD and PRWALD, respectively.

The OUTFILENAME parameter can be used to save the Wald statistics and the QEFFECTS and QSE structures in a Genstat work book file in a sheet named STATISTICS. This parameter should not contain an extension as the extension is defined automatically as .gwb.

The QSAVE parameter can be used to save a pointer containing information and results for the significant QTLs. The elements of the pointer are labelled as follows to simplify their subsequent use:

The elements 'procedure', 'trait', 'markernames', 'chromosomes', 'envnames', 'idlfm', 'idrfm', 'idlfmci' and 'idrfmci' are text structures; 'positions', 'waldstatistics', 'prwald', 'dfwald', 'lowerci', 'upperci', 'posmin', 'posmax', 'posminci, 'posmaxci', 'vexplained' and 'locus' are variates; 'qeffects' and 'qse' are pointers (see parameters QEFFECTS and QSE); and 'neff' is a scalar.

The SAVE parameter can be used to save the REML save structure from the analysis for use with subsequent VKEEP and VDISPLAY directives.

Options: PRINT, POPULATIONTYPE, NGENERATIONS, NBACKCROSSES, NSELFINGS, FIXED, UNITFACTOR, MVINCLUDE, MAXCYCLE, WORKSPACE.

Parameters: TRAIT, GENOTYPES, UNITERROR, ADDITIVEPREDICTORS, ADD2PREDICTORS, DOMINANCEPREDICTORS, CHROMOSOMES, POSITIONS, IDLOCI, MKLOCI, IDMGENOTYPES, IDPARENTS, QTLSELECTED, RESIDUALS, FITTEDVALUES, WALDSTATISTICS, PRWALD, QEFFECTS, QSE, OUTFILENAME, QSAVE, SAVE.

Method

QSESTIMATE fits the following models which include a set L of QTLs:

1)       y_i = μ + Σ_l∈L x_il^add α_l^add + G_i

if only ADDITIVEPREDICTORS are specified

2)       y_i = μ + Σ_l∈L ( x_il^add α_l^add + x_il^dom α_l^dom ) + G_i

if DOMINANCEPREDICTORS are also specified

3)       y_i = μ + Σ_l∈L ( x_il^add α_l^add + x_il^add2 α_l^add2 + x_il^dom α_l^dom ) + G_i

if both ADD2PREDICTORS and DOMINANCEPREDICTORS are specified (for population type CP)

where y_i is the trait value of genotype i, x_il^add are the additive genetic predictors of genotype i for locus l, and α^add are the associated effects. In models 2 and 3, x_il^dom are the dominance genetic predictors, and α_l^add are the associated effects. In model 3, x_il^add are the additive genetic predictors for maternal genotype i at locus l, x_il^add2 are the additive genetic predictors for paternal genotype i, and α^add and α^add2 are the associated effects. Genetic predictors are genotypic covariables that reflect the genotypic composition of a genotype at a specific chromosome location (Lynch & Walsh 1998). G_i is the residual unexplained genetic and environmental variation, which is assumed to follow a Normal distribution with mean 0 and variance σ².

Action with RESTRICT

Restrictions are not allowed.

Reference

Lynch, M. & Walsh, B. (1998). Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.

See also

Procedures: QSBACKSELECT, QSQTLSCAN, QFLAPJACK, QREPORT.

Commands for: Statistical genetics and QTL estimation.

Example

CAPTION    'QSESTIMATE example'; STYLE=meta
SPLOAD     [PRINT=*] '%GENDIR%/Examples/F2maize_traits.gsh'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='LOCI'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='ADDPREDICTORS'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='DOMPREDICTORS'
" create single environment "
SUBSET     [E.EQ.6] G,yld
" Candidate QTL positions from QSBACKSELECT "
VARIATE    [VALUES=19,111,237] Qid
VARIATE    [VALUES=0,1,0] Domid
QSESTIMATE [PRINT=summary,model,wald,effects; POPULATIONTYPE=F2]\ 
           TRAIT=yld; GENOTYPES=G; CHROMOSOMES=mkchr; POSITIONS=mkpos;\ 
           IDLOCI=idlocus; MKLOCI=marker;\
           ADDITIVEPREDICTORS=addpred; DOMINANCEPREDICTORS=dompred;\ 
           QTLSELECTED=Qid; DOMSELECTED=Domid; QEFFECTS=qeff; QSE=qse;\ 
           QSAVE=Output; OUTFILENAME='F2maize_qsestimate'